Z Score Calculator

An R script for quick calculation of Z-scores, fold change, median, mean, SD, per million counts, and gene quality filters in gene expression data. Simplify your bioinformatics analysis.

sanmatidugad
1
0
R

Z-Score-Calculator

Command-Line

Rscript Z_analysis.R \
-i -normalized.txt \
-s -gene-states.csv \
-gc subsampled.gc_totals.csv \
-n normal_count \
-a actionable genes \

where:

-i = normalized gene count output file
-s = gene states output file (generated by secondary pipeline)
-gc = gene count file generated after subsampling
-n = numeric value mentioning the number of normal samples in the project
-a = file containing a specific list of genes that should be selected for analysis.

Specific Considerations for Data Preparation

  1. All data should first contain normal samples followed by tumor samples
  2. The Gene ID column should be default named as “SYMBOL”
  3. First Column should Contain ENSEMBL IDs with no duplicates.